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As part of the iCloud services in macOS Sierra, Apple is offering a new way to store your files in iCloud – synchronizing the contents of your account’s Desktop and Documents folder with iCloud Drive.

When you enable the option to store files from your Desktop and Documents folder, the contents of your Desktop and Documents folder are moved (not copied) from your home folder into iCloud Drive. Those folders will no longer appear in your home folder.

That means that your Desktop and Documents folder no longer are stored in your home folder. Instead, they and all their contents are now stored in iCloud Drive.